Difference between revisions of "Amino acid"

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(→‎Reduced (redundant or simplified) alphabets for proteins)
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  IVLFCMAW => P: Hydrophilic
 
  IVLFCMAW => P: Hydrophilic
 
  GTSYPM  => N: Neutral
 
  GTSYPM  => N: Neutral
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  DNEQKR  =>H: Hydrophobic
+
  DNEQKR  => H: Hydrophobic
  
 
*Five letters alphabet: Chemical / structural properties<ref name="Pommie2004">Pommié C, Levadoux S, Sabatier R, Lefranc G & Lefranc MP (2004). "IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties". ''Journal of Molecular Recognition, 17:17-32''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14872534&dopt=Abstract PMID: 14872534]</ref>
 
*Five letters alphabet: Chemical / structural properties<ref name="Pommie2004">Pommié C, Levadoux S, Sabatier R, Lefranc G & Lefranc MP (2004). "IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties". ''Journal of Molecular Recognition, 17:17-32''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14872534&dopt=Abstract PMID: 14872534]</ref>

Revision as of 02:34, 16 May 2012

In chemistry, an amino acid is a molecule that contains both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids with the general formula NH2CHRCOOH.[1]

Amino acid atoms

The following atoms are expected for a given amino acid: 

 aa   1 2  3 4 5  6   7   8   9   10  11  12  13  14 
 A:   N CA C O CB                                      : Alanine
 V:   N CA C O CB CG1 CG2                              : Valine
 L:   N CA C O CB CG  CD1 CD2                          : Leucine
 I:   N CA C O CB CG1 CG2 CD1                          : Isoleucine
 P:   N CA C O CB CG  CD                               : Proline
 M:   N CA C O CB CG  SD  CE                           : Methionine
 F:   N CA C O CB CG  CD1 CD2 CE1 CE2 CZ               : Phenylalanine
 W:   N CA C O CB CG  CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2  : Tryptophan
 G:   N CA C O                                         : Glycine
 S:   N CA C O CB OG                                   : Serine
 T:   N CA C O CB OG1 CG2                              : Threonine
 C:   N CA C O CB SG                                   : Cysteine
 Y:   N CA C O CB CG  CD1 CD2 CE1 CE2 CZ  OH           : Tyrosine
 N:   N CA C O CB CG  OD1 ND2                          : Asparagine
 Q:   N CA C O CB CG  CD  OE1 NE2                      : Glutamine
 D:   N CA C O CB CG  OD1 OD2                          : Aspartic acid
 E:   N CA C O CB CG  CD  OE1 OE2                      : Glutamic acid
 K:   N CA C O CB CG  CD  CE  NZ                       : Lysine
 R:   N CA C O CB CG  CD  NE  CZ  NH1 NH2              : Arginine
 H:   N CA C O CB CG  ND1 CD2 CE1 NE2                  : Histidine
 X:   N CA C O CB                                      : Nonstandard (ATOM or HETATM records)
 #:   N CA C O                                         : Unknown (ATOM records)

Reduced (redundant or simplified) alphabets for proteins

AGTSNQDEHRKP => P: Hydrophilic
CMFILVWY     => H: Hydrophobic
  • Five letters alphabet: Chemical / structural properties[4]
IVL   => A: Aliphatic
FYWH  => R: Aromatic
KRDE  => C: Charged
GACS  => T: Tiny
TMQNP => D: Diverse
  • Six letters alphabet: Chemical / structural properties #2[4]
IVL   => A: Aliphatic
FYWH  => R: Aromatic
KR    => C: Pos. charged
DE    => C: Neg. charged
GACS  => T: Tiny
TMQNP => D: Diverse
  • 3 IMGT amino acid hydropathy alphabet[5]
IVLFCMAW => P: Hydrophilic
GTSYPM   => N: Neutral
DNEQKR   => H: Hydrophobic
  • Five letters alphabet: Chemical / structural properties[5]
IVL   => A: Aliphatic
FYWH  => R: Aromatic
KRDE  => C: Charged
GACS  => T: Tiny
TMQNP => D: Diverse5 IMGT amino acid volume alphabet
GAS   => G: 60-90
CDPNT => C: 108-117
EVQH  => E: 138-154
MILKR => M: 162-174
FYW   => F: 189-228
  • 11 IMGT amino acid chemical characteristics alphabet[5]
AVIL => A: Aliphatic
F    => F: Phenylalanine
CM   => C: Sulfur
G    => G: Glycine
ST   => S: Hydroxyl
W    => W: Tryptophan
Y    => Y: Tyrosine
P    => P: Proline
DE   => A: Acidic
NQ   => N: Amide
HKR  => H: Basic
  • Murphy et al., 2000; 15 letters alphabet[6]
LVIM => L: Large hydrophobic
C    => C
A    => A
G    => G
S    => S
T    => T
P    => P
FY   => F: Hydrophobic/aromatic sidechains
W    => W
E    => E
D    => D
N    => N
Q    => Q
KR   => K: Long-chain positively charged
H    => H
  • Murphy et al., 2000; 10 letters alphabet[6]
LVIM => L: Large hydrophobic
C    => C
A    => A
G    => G
ST   => S: Polar
P    => P
FYW  => F:Hydrophobic/aromatic sidechains
EDNQ => E: Charged / polar
KR   => K: Long-chain positively charged
H    => H
  • Murphy et al., 2000; 8 letters alphabet[6]
LVIMC => L: Hydrophobic
AG    => A
ST    => S: Polar
P     => P
FYW   => F: Hydrophobic/aromatic sidechains
EDNQ  => E
KR    => K: Long-chain positively charged
H     => H
  • Murphy et al., 2000; 4 letters alphabet[6]
LVIMC   => L: Hydrophobic
AGSTP   => A
FYW     => F: Hydrophobic/aromatic sidechains
EDNQKRH => E
  • Murphy et al., 2000; 2 letters alphabet[6]
LVIMCAGSTPFYW => P: Hydrophobic
EDNQKRH       => E: Hydrophilic
  • Wang & Wang, 1999; 5 letters alphabet[7]
CMFILVWY => I
ATH      => A
GP       => G
DE       => E
SNQRK    => K
  • Wang & Wang, 1999; 5 letters variant alphabet[7]
CMFI => I
LVWY => L
ATGS => A
NQDE => E
HPRK => K
  • Wang & Wang, 1999; 3 letters alphabet[7]
CMFILVWY => I
ATHGPR   => A
DESNQK   => E
  • Wang & Wang, 1999; 2 letters alphabet[7]
CMFILVWY     => I
ATHGPRDESNQK => A
  • Li et al., 2003; 10 letters alphabet[8]
C   => C
FYW => Y
ML  => L
IV  => V
G   => G
P   => P
ATS => S
NH  => N
QED => E
RK  => K
  • Li et al., 2003; 5 letters alphabet[8]
CFYW    => Y
MLIV    => I
G       => G
PATS    => S
NHQEDRK => E
  • Li et al., 2003; 4 letters alphabet[8]
CFYW    => Y
MLIV    => I
GPATS   => S
NHQEDRK => E
  • Li et al., 2003; 3 letters alphabet[8]
CFYWMLIV => I
GPATS    => S
NHQEDRK  => E

References

  1. ↑ Proline is an exception to this general formula. It lacks the NH2 group because of the cyclization of the side chain.
  2. ↑ Chan HS, Dill KA (1989). "Compact polymers". Macromolecules, 22:4559-4573.
  3. ↑ Lau KF, Dill KA (1989). "A lattice statistical mechanics model of the conformational and sequence spaces of proteins". Macromolecules, 22:3986-3997.
  4. ↑ 4.0 4.1 Betts MJ, Russell RB (2003). "Amino acid properties and consequences of subsitutions". Bioinformatics for Geneticists, M.R. Barnes, I.C. Gray eds, Wiley.
  5. ↑ 5.0 5.1 5.2 Pommié C, Levadoux S, Sabatier R, Lefranc G & Lefranc MP (2004). "IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties". Journal of Molecular Recognition, 17:17-32. PMID: 14872534
  6. ↑ 6.0 6.1 6.2 6.3 6.4 Murphy LR, Wallqvist A, Levy RM (2000). "Simplified amino acid alphabets for protein fold recognition and implications for folding". Protein Eng, 13:149-152. PMID: 10775656
  7. ↑ 7.0 7.1 7.2 7.3 Wang J, Wang W (1999). "A computational approach to simplifying the protein folding alphabet". Nat Struct Biol, 11:1033-1038. PMID: 10542095
  8. ↑ 8.0 8.1 8.2 8.3 Li T, Fan K, Wang J, Wang W (2003). "Reduction of protein sequence complexity by residue grouping". Protein Eng, 5:323-330. PMID: 12826723

Further reading

  • Spitzer M, Fuellen G, Cullen P, Lorkowski S (2004). "VisCoSe: visualization and comparison of consensus sequences". Bioinformatics, 20:433-435. PMID: 14960475.
  • Livingstone CD, Barton GJ (1993). "Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation". Comput Appl Biosci, 9(6):745-56. PMID: 8143162.

External links

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